From 525c1a9e6d5a33075669085148247e2604dd092f Mon Sep 17 00:00:00 2001
From: manonBlanco <blanco@teklia.com>
Date: Fri, 24 Nov 2023 13:18:51 +0100
Subject: [PATCH] Comply with ruff's PT rule
---
nerval/evaluate.py | 2 +-
pyproject.toml | 2 +
tests/conftest.py | 20 +++---
tests/{ => fixtures}/test_mapping_file.csv | 0
tests/test_align.py | 2 +-
tests/test_compute_matches.py | 2 +-
tests/test_compute_scores.py | 2 +-
tests/test_folder/test_demo_annot.bio | 82 ----------------------
tests/test_folder/test_demo_predict.bio | 81 ---------------------
tests/test_folder/test_toy_annot.bio | 39 ----------
tests/test_folder/test_toy_predict.bio | 39 ----------
tests/test_get_labels_aligned.py | 2 +-
tests/test_parse_bio.py | 30 +++++---
tests/test_run.py | 31 +++++---
14 files changed, 56 insertions(+), 278 deletions(-)
rename tests/{ => fixtures}/test_mapping_file.csv (100%)
delete mode 100644 tests/test_folder/test_demo_annot.bio
delete mode 100644 tests/test_folder/test_demo_predict.bio
delete mode 100644 tests/test_folder/test_toy_annot.bio
delete mode 100644 tests/test_folder/test_toy_predict.bio
diff --git a/nerval/evaluate.py b/nerval/evaluate.py
index 7feec7b..5afe7cc 100644
--- a/nerval/evaluate.py
+++ b/nerval/evaluate.py
@@ -374,7 +374,7 @@ def run_multiple(file_csv: Path, folder: Path, threshold: int, verbose: bool):
recall += scores["All"]["R"]
f1 += scores["All"]["F1"]
else:
- raise Exception(f"No file found for files {annot}, {predict}")
+ raise Exception(f"No file found for files {row[0]}, {row[1]}")
if count:
logger.info("Average score on all corpus")
table = PrettyTable()
diff --git a/pyproject.toml b/pyproject.toml
index 28ef1df..24be6f8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -35,4 +35,6 @@ select = [
"ARG",
# flake8-use-pathlib
"PTH",
+ # flake8-pytest-style
+ "PT",
]
diff --git a/tests/conftest.py b/tests/conftest.py
index 5381d25..61b7300 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -5,46 +5,46 @@ import pytest
FIXTURES = Path(__file__).parent / "fixtures"
-@pytest.fixture
+@pytest.fixture()
def fake_annot_bio():
return FIXTURES / "test_annot.bio"
-@pytest.fixture
+@pytest.fixture()
def fake_predict_bio():
return FIXTURES / "test_predict.bio"
-@pytest.fixture
+@pytest.fixture()
def empty_bio():
return FIXTURES / "test_empty.bio"
-@pytest.fixture
+@pytest.fixture()
def bad_bio():
return FIXTURES / "test_bad.bio"
-@pytest.fixture
+@pytest.fixture()
def bioeslu_bio():
return FIXTURES / "bioeslu.bio"
-@pytest.fixture
+@pytest.fixture()
def end_of_file_bio():
return FIXTURES / "end_of_file.bio"
-@pytest.fixture
+@pytest.fixture()
def nested_bio():
return FIXTURES / "test_nested.bio"
-@pytest.fixture
+@pytest.fixture()
def folder_bio():
- return Path("test_folder")
+ return FIXTURES
@pytest.fixture()
def csv_file():
- return Path("test_mapping_file.csv")
+ return FIXTURES / "test_mapping_file.csv"
diff --git a/tests/test_mapping_file.csv b/tests/fixtures/test_mapping_file.csv
similarity index 100%
rename from tests/test_mapping_file.csv
rename to tests/fixtures/test_mapping_file.csv
diff --git a/tests/test_align.py b/tests/test_align.py
index 35be3ba..14725f2 100644
--- a/tests/test_align.py
+++ b/tests/test_align.py
@@ -3,7 +3,7 @@ import pytest
@pytest.mark.parametrize(
- "query,target",
+ ("query", "target"),
[
(
"Gérard de Nerval was born in Paris in 1808 .",
diff --git a/tests/test_compute_matches.py b/tests/test_compute_matches.py
index 270c448..2cd8586 100644
--- a/tests/test_compute_matches.py
+++ b/tests/test_compute_matches.py
@@ -202,7 +202,7 @@ fake_predict_tags_bk_boundary_2 = [
@pytest.mark.parametrize(
- "test_input, expected",
+ ("test_input", "expected"),
[
(
(
diff --git a/tests/test_compute_scores.py b/tests/test_compute_scores.py
index d51af08..239754f 100644
--- a/tests/test_compute_scores.py
+++ b/tests/test_compute_scores.py
@@ -4,7 +4,7 @@ from nerval import evaluate
@pytest.mark.parametrize(
- "annot,predict,matches",
+ ("annot", "predict", "matches"),
[
(
{"All": 3, "DAT": 1, "LOC": 1, "PER": 1},
diff --git a/tests/test_folder/test_demo_annot.bio b/tests/test_folder/test_demo_annot.bio
deleted file mode 100644
index cf16200..0000000
--- a/tests/test_folder/test_demo_annot.bio
+++ /dev/null
@@ -1,82 +0,0 @@
-Césaire B-PER
-Alphonse I-PER
-Garon I-PER
-marraine O
-Adeline B-PER
-Dionne I-PER
-, O
-soussignés O
-Lecture O
-faite O
-Adéline O
-Dionne O
-Arsène O
-Côté O
-Arpin O
-R O
-Le O
-onze B-DAT
-aout I-DAT
-mil I-DAT
-neuf I-DAT
-cent I-DAT
-un I-DAT
-nous O
-prêtre O
-soussigné O
-avons O
-baptisé O
-Marie B-PER
-Luce I-PER
-Louise I-PER
-, O
-née O
-la B-DAT
-veille I-DAT
-, O
-fille O
-légitime O
-de O
-Carmel B-PER
-Côté I-PER
-, O
-cordonnier B-OCC
-, O
-pré O
-- O
-sent O
-, O
-déclarant O
-ne O
-savoir O
-signer O
-, O
-et O
-de O
-Eugé B-PER
-nie I-PER
-Fréchette I-PER
-, O
-de O
-cette B-LOC
-paroisse I-LOC
-. O
-Parrain O
-Napoléon B-PER
-Fréchette I-PER
-, O
-marraine O
-Adeline B-PER
-Tremblay I-PER
-, O
-soussignés O
-, O
-de O
-Ste B-LOC
-Luce I-LOC
-, O
-Lec O
-- O
-ture O
-faite O
-. O
diff --git a/tests/test_folder/test_demo_predict.bio b/tests/test_folder/test_demo_predict.bio
deleted file mode 100644
index 7e01c2d..0000000
--- a/tests/test_folder/test_demo_predict.bio
+++ /dev/null
@@ -1,81 +0,0 @@
-Césaire B-PER
-Alphonse O
-Garon B-PER
-marraine O
-Adeline B-PER
-Dionne I-PER
-, O
-soussignés O
-Lecture O
-faite O
-Adéline O
-Dionne O
-Arsène O
-Côté O
-Arpin O
-R O
-Le O
-onze B-DAT
-aout I-DAT
-mil I-DAT
-neuf I-DAT
-cent I-DAT
-un O
-nous O
-pretre O
-soussigné O
-avons O
-baptisé O
-Marie B-PER
-Luce I-PER
-Louise I-PER
-, O
-née O
-la B-DAT
-veille I-DAT
-, O
-fille O
-légitime O
-de O
-Carmel B-PER
-Côté I-PER
-, O
-cordonnier B-OCC
-, O
-pré O
-- O
-sent O
-, O
-déclarant O
-ne O
-savoir O
-signer O
-, O
-et O
-de O
-Eugé B-PER
-nie I-PER
-Fréchette I-PER
-, O
-de O
-cette B-LOC
-paroisse I-LOC
-. O
-Parrain O
-Napoléon B-PER
-Fréchette I-PER
-, O
-marraine O
-Adéline B-PER
-Tremblay I-PER
-, O
-sousignés O
-, O
-de O
-St B-LOC
-. I-LOC
-Luce O
-, O
-Lec O
-ture O
-faite O
diff --git a/tests/test_folder/test_toy_annot.bio b/tests/test_folder/test_toy_annot.bio
deleted file mode 100644
index 5a941ee..0000000
--- a/tests/test_folder/test_toy_annot.bio
+++ /dev/null
@@ -1,39 +0,0 @@
-John B-PER
-Ronald I-PER
-Reuel I-PER
-Tolkien I-PER
-was O
-born O
-on O
-three B-DAT
-January I-DAT
-eighteen I-DAT
-ninety I-DAT
-- I-DAT
-two I-DAT
-in O
-Bloemfontein B-LOC
-in O
-the O
-Orange B-LOC
-Free I-LOC
-State I-LOC
-, O
-to O
-Arthur B-PER
-Reuel I-PER
-Tolkien I-PER
-, O
-an O
-English O
-bank B-OCC
-manager I-OCC
-, O
-and O
-his O
-wife O
-Mabel B-PER
-, O
-née O
-Suffield B-PER
-. O
diff --git a/tests/test_folder/test_toy_predict.bio b/tests/test_folder/test_toy_predict.bio
deleted file mode 100644
index 5a941ee..0000000
--- a/tests/test_folder/test_toy_predict.bio
+++ /dev/null
@@ -1,39 +0,0 @@
-John B-PER
-Ronald I-PER
-Reuel I-PER
-Tolkien I-PER
-was O
-born O
-on O
-three B-DAT
-January I-DAT
-eighteen I-DAT
-ninety I-DAT
-- I-DAT
-two I-DAT
-in O
-Bloemfontein B-LOC
-in O
-the O
-Orange B-LOC
-Free I-LOC
-State I-LOC
-, O
-to O
-Arthur B-PER
-Reuel I-PER
-Tolkien I-PER
-, O
-an O
-English O
-bank B-OCC
-manager I-OCC
-, O
-and O
-his O
-wife O
-Mabel B-PER
-, O
-née O
-Suffield B-PER
-. O
diff --git a/tests/test_get_labels_aligned.py b/tests/test_get_labels_aligned.py
index b4daa39..4e0650e 100644
--- a/tests/test_get_labels_aligned.py
+++ b/tests/test_get_labels_aligned.py
@@ -97,7 +97,7 @@ expected_predict_tags_aligned = [
@pytest.mark.parametrize(
- "test_input, expected",
+ ("test_input", "expected"),
[
(
(fake_annot_original, fake_annot_aligned, fake_annot_tags_original),
diff --git a/tests/test_parse_bio.py b/tests/test_parse_bio.py
index 66f8957..5f80734 100644
--- a/tests/test_parse_bio.py
+++ b/tests/test_parse_bio.py
@@ -1,3 +1,5 @@
+import re
+
import pytest
from nerval import evaluate
@@ -168,7 +170,7 @@ expected_parsed_end_of_file = {
@pytest.mark.parametrize(
- "test_input, expected",
+ ("test_input", "expected"),
[
(pytest.lazy_fixture("fake_annot_bio"), expected_parsed_annot),
(pytest.lazy_fixture("fake_predict_bio"), expected_parsed_predict),
@@ -183,18 +185,21 @@ def test_parse_bio(test_input, expected):
def test_parse_bio_bad_input(bad_bio):
- with pytest.raises(Exception):
- evaluate.parse_bio(bad_bio)
+ lines = bad_bio.read_text().strip().splitlines()
+ with pytest.raises(
+ Exception, match=re.escape("The file is not in BIO format: check line 1 (file)")
+ ):
+ evaluate.parse_bio(lines)
@pytest.mark.parametrize(
- "line, word, label",
- (
+ ("line", "word", "label"),
+ [
("Hi B-ORG", "Hi", "B-ORG"),
("Hi B-Org or maybe not org", "Hi", "B-Org or maybe not org"),
("1258 B-Date et Lieu", "1258", "B-Date et Lieu"),
("Devoti B-Sous-titre", "Devoti", "B-Sous-titre"),
- ),
+ ],
)
def test_parse_line(line, word, label):
assert parse_line(index=0, line=line) == (word, label)
@@ -202,21 +207,24 @@ def test_parse_line(line, word, label):
@pytest.mark.parametrize(
"line",
- (("HiB-ORG"), ("HiB-ORG or maybe not")),
+ [("HiB-ORG"), ("HiB-ORG or maybe not")],
)
def test_parse_line_crash(line):
- with pytest.raises(Exception):
+ with pytest.raises(
+ Exception,
+ match=re.escape(f"The file is not in BIO format: check line 0 ({line})"),
+ ):
parse_line(index=0, line=line)
@pytest.mark.parametrize(
- "label, expected_type",
- (
+ ("label", "expected_type"),
+ [
("B-ORG", "ORG"),
("B-Date et Lieu", "Date et Lieu"),
("I-Date et Lieu", "Date et Lieu"),
("B-Sous-titre", "Sous-titre"),
- ),
+ ],
)
def test_get_type_label(label, expected_type):
assert get_type_label(label) == expected_type
diff --git a/tests/test_run.py b/tests/test_run.py
index 2381dd6..63b8ebe 100644
--- a/tests/test_run.py
+++ b/tests/test_run.py
@@ -1,11 +1,14 @@
+import re
+from pathlib import Path
+
import pytest
from nerval import evaluate
@pytest.mark.parametrize(
- "annotation, prediction, expected",
- (
+ ("annotation", "prediction", "expected"),
+ [
(
pytest.lazy_fixture("fake_annot_bio"),
pytest.lazy_fixture("fake_predict_bio"),
@@ -82,7 +85,7 @@ from nerval import evaluate
},
},
),
- ),
+ ],
)
def test_run(annotation, prediction, expected):
assert (
@@ -97,16 +100,22 @@ def test_run(annotation, prediction, expected):
def test_run_empty_bio(empty_bio):
- with pytest.raises(Exception):
- evaluate.run(empty_bio, empty_bio, 0.3)
+ with pytest.raises(
+ Exception, match="No content found in annotation or prediction files."
+ ):
+ evaluate.run(empty_bio, empty_bio, 0.3, False)
def test_run_empty_entry():
- with pytest.raises(TypeError):
- evaluate.run(None, None, 0.3)
+ with pytest.raises(
+ AssertionError,
+ match=re.escape("Error: Input file invalid.bio does not exist"),
+ ):
+ evaluate.run(Path("invalid.bio"), Path("invalid.bio"), 0.3, False)
-@pytest.mark.parametrize("threshold", ([0.3]))
-def test_run_multiple(csv_file, folder_bio, threshold):
- with pytest.raises(Exception):
- evaluate.run_multiple(csv_file, folder_bio, threshold)
+def test_run_multiple(csv_file, folder_bio):
+ with pytest.raises(
+ Exception, match="No file found for files demo_annot.bio, demo_predict.bio"
+ ):
+ evaluate.run_multiple(csv_file, folder_bio, 0.3, False)
--
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